## [1] "O77_p5_IFNg_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
69,545,581 |
69,545,581 |
| Not Truncated |
40,427,228 |
40,342,336 |
| Truncated |
29,118,353 |
29,203,245 |
Truncated Read Length
| Average Length Truncated |
40 |
39.9 |
Mapping Efficiency
| Too Short To Map |
8,237,036 |
8,703,456 |
| Unique Alignments |
56,273,429 |
53,300,235 |
| Multiple Alignments |
2,096,046 |
2,824,716 |
| Failed To Align |
2,939,070 |
4,717,174 |
| Paired |
43,129,800 |
43,129,800 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
16,280,045 |
| Invalid Pairs |
26,849,755 |
| Same Circularised |
210,844 |
| Same Dangling Ends |
3,449,351 |
| Same Fragment Internal |
12,977,003 |
| Re Ligation |
8,782,414 |
| Contiguous Sequence |
212,669 |
| Wrong Size |
1,217,474 |
| Total Pairs |
43,129,800 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
16,280,045 |
31,666 |
| Cis-close (<10Kbp) |
1,379,170 |
2,905 |
| Cis-far (>10Kbp) |
9,252,176 |
16,724 |
| Trans |
5,648,699 |
12,037 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
